Directed evolution of 3D printed microbial communities

这个项目研究了细胞的空间排列在反硝化中的作用，反硝化是一个在生物技术中有重要应用的中心生态系统过程。细菌在生物技术和生态系统的运作中都发挥着至关重要的作用。这些微生物以特定的空间模式组织起来，并经常在社区内相互作用。众所周知，空间组织是不同物种如何相互作用以及群落最终功能的核心。然而，微生物生态学中的一个关键挑战是了解空间网络的不同方面如何对整体功能做出贡献。研究这一问题的两个主要挑战是大量可能的空间安排和在太空中操纵微生物的困难。为了克服这些挑战，这项研究使用进化算法来有效地探索不同的空间排列，并使用一种新的方法在3D中打印微生物群落，从而可以更好地进行系统操作。这些方法被用来研究不同微生物的空间组织如何影响反硝化过程，反硝化是氮循环中的一个重要步骤，影响生态系统和耕作土壤中氮素的有效性。该项目促进了对微生物群落及其功能的理解。它对空间结构在氮循环中的作用提供了洞察，为土壤研究和废水处理应用提供了信息。此外，本研究开发的3D打印方法可以很容易地适用于其他类型的社区及其功能的研究。该项目的一个不可或缺的组成部分是为不同的学生群体提供跨学科的指导，并通过不同的科学教育计划和与当地社区的接触来增加获得科学和技术的机会。微生物群落对我们的健康和生态系统的健康具有重要的作用。其中许多功能是在空间结构的微生物群落中执行的，如生物膜、微生物垫和土壤团聚体。虽然众所周知，空间结构可以影响群落的功能和相互作用，但人们对不同单元在空间中的排列如何影响群落的功能的了解有限。解决这一问题的两个重要限制是，即使是最简单的社区，可能的参数和构象的空间也很大，以及缺乏构建预定义的、稳定的空间社区的技术。这项研究通过实验和计算构建了预定义的细菌空间群落，并探索了细胞的空间排列对群落的功能、稳定性和分工的影响。模式细菌群落由一系列可培养的细菌组成，这些细菌能够执行反硝化途径的不同步骤。虽然反硝化可以完全由单一物种完成，但它往往是由多个细菌物种通过分工来执行的，这使其成为理想的模式系统。该研究项目开发了空间显式的反硝化计算机模拟，扩展了一种新型的聚合物支架系统，以预先指定的空间组织打印整个反硝化微生物群落，并使用进化算法在二维和三维选择不同的改进功能的空间构象。通过使用脚手架系统通过生物打印来评估这些构象来评估算法。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

This project investigates the role of the spatial arrangement of cells in denitrification, a central ecosystem process with important applications in biotechnology. Bacteria play a crucial role in both biotechnology and the functioning of ecosystems. These microbes are organized in specific spatial patterns and often interact with each other within communities. It is known that spatial organization is central to how different species interact and to the resulting function of the community. However, a key challenge in microbial ecology is understanding how different aspects of the spatial network contribute to the overall function. The two main challenges in studying this problem are the vast number of possible spatial arrangements and the difficulty of manipulating microbes in space. To overcome these challenges, this research uses evolutionary algorithms to efficiently explore different spatial arrangements, and a novel approach to print microbial communities in 3D which allows better system manipulation. These approaches are used to investigate how the spatial organization of different microbes affects the process of denitrification, an essential step in the nitrogen cycle, impacting the availability of nitrogen in ecosystems and farming soils. This project advances the understanding of microbial communities and their function. It provides insight into the role of spatial structure on nitrogen cycling, informing soil research and applications for waste-water treatment. Moreover, the 3D printing approach developed in this research can be easily adapted to study other types of communities and their functions. An indispensable component of this project is providing interdisciplinary mentorship to diverse groups of students and increasing access to science and technology through different science education programs and outreach to local communities. Microbial communities perform important functions for our health and that of ecosystems. Many of these functions are performed in spatially structured microbial communities such as biofilms, microbial mats and soil aggregates. While it is well known that spatial structure can affect community functions and interactions, there is limited understanding of how the arrangement of different cells in space influences the function of the community. Two important limitations in addressing this question are the large space of possible parameters and conformations for even the simplest community and a lack of technology to construct a pre-defined, stable spatial community. The research constructs pre-defined spatial communities of bacteria, both experimentally and computationally, and explores the effect of cells’ spatial arrangement on a community’s function, stability, and division of labor. The model bacterial community is composed of a mix of culturable species of bacteria able to perform different steps of the denitrification pathway. While denitrification could be performed entirely by a single species, it is often performed by multiple bacterial species through division of labor, making it an ideal model system. This research project develops a spatially explicit computer simulation of denitrification, expands a novel polymer scaffold system to print entire denitrifying microbial communities with pre-specified spatial organization and uses evolutionary algorithms to select different spatial conformations of improved function in two and three dimensions. Algorithms are evaluated by assessing these conformations through bio-printing with the scaffold system.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.